Nucleic acid base pairing

The purines and the pyrimidines are complementary bases. The pairings of the bases are as follows:

Guanine is the complement of cytosine.
Adenine is the complement of thymine in DNA and uracil in RNA.

Thus, the fraction of one base must be equal to the fraction of its complement the complementary strand. This is known as the Chargaff's rule.

A biochemist is given a single strand of DNA with a base composition of 35% guanine. His task is to create a complement strand of DNA. According to Chargaff's rule the complementary strand must have a base cmposition of 35% cytosine!

The base pairing gives very precise geometry. The distance between the C1' of a base and the C1' of its complement is exactly 10.85 angstrom. The angle formed by the bond between the c1' and n9 and a line connecting the c1's of the complementary bases are all 51.5 degrees. This is expected since the double helix structure, when viewed from above, is circular with a diameter of 10.85 angstrom.

Because of the presence of an extra site for hydrogen bonding, the guanine-cytosine base pairing is found to be more stable than the adenine-thymine pairing. Thus, if a DNA strand is found to be rich in guanine and cytosine, then more energy will be needed to denature the DNA (i.e., to destroy the double helix structure). If a biochemist were given two strands of DNA of equal length, but of different base composition with Strand 'a' having a high guanine and cytosine fraction than Strand 'b', Strand 'b' should denature at a lower temperature, since 'b' has a lower g-c fraction, there is less hydrogen bonds to break. thus less energy is required!

It has been found that DNA double helix can exist in three different forms. they are known as:
A DNA
B DNA
Z DNA
The difference between the three different DNA forms are its geometry. In the 'a DNA' the angle between two successive bases on a strand is 32.7# degrees, whereas for the 'b DNA' the angle is 36 degree. In the 'b DNA' the plane containing the base and its complement is parallel to other planes containing a base pair. Whereas in the 'a DNA' this does not hold. The information on the 'z DNA' is not available, but recent research suggests that DNA exists in this form when it is actively being transcribed Into mRNA's. This result is not too surprising since 'z DNA' is a metastable configuration for DNA.


This was orininally a BASIC program written by Bill Chan for his term project.